99 cougar has a miss

My 99 cougar has a miss. I just recently installed a K and N cold air intake. It has new plugs and wires. I was wondering if the new intake might be causing a compression issue... and if so... how would i check for that. Car has 3 and a half inch apexi ehaust from dc comp headers back. so it has always idled kinda rough... but now when you first start the car it tries to stall. She stutters in first and second gear while accelerating too. Oh and one more thing. Im not sure about the check engine light flashing. I know it flashes when it has a miss but it doesnt flash consitently. It does it intermittently. The light is always on because she runs off of a fuel cell in the trunk and runs rich. But the light only flashes every now and then. Any thoughts or advice on the topic would be grealy appreciated. It has the 2.5 liter v6. 5 speed.
V/R
Edward Lewis